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Package Maintainer Title
ACME Sean Davis Algorithms for Calculating Microarray Enrichment (ACME)
adSplit Claudio Lottaz Annotation-Driven Clustering
affyContam V. Carey structured corruption of affymetrix cel file data
AffyExpress Xuejun Arthur Li Affymetrix Quality Assessment and Analysis Tool
affylmGUI Keith Satterley GUI for affy analysis using limma package
arrayMvout V. Carey multivariate outlier detection for expression array QA
ArrayTools Arthur Li geneChip Analysis Package
BAC Raphael Gottardo Bayesian Analysis of Chip-chip experiment
BCRANK Adam Ameur Predicting binding site consensus from ranked DNA sequences
bgafun Iain Wallace BGAfun A method to identify specifity determining residues in protein families
BGmix Alex Lewin Bayesian models for differential gene expression
BicARE Pierre Gestraud , BicARE
Biobase Biocore Team c/o BioC user list Biobase: Base functions for Bioconductor
BiocCaseStudies Biocore Team c/o BioC user list BiocCaseStudies: Support for the Case Studies Monograph
bioDist Biocore Team c/o BioC user list Different distance measures
Biostrings H. Pages String objects representing biological sequences, and matching algorithms
Category Robert Gentleman Category Analysis
ChemmineR Y. Eddie Cao A Compound Data Mining Framework
clusterStab James W. MacDonald Compute cluster stability scores for microarray data
CMA Martin Slawski Synthesis of microarray-based classification
CoCiteStats R. Gentleman Different test statistics based on co-citation.
CORREP Dongxiao Zhu Multivariate Correlation Estimator and Statistical Inference Procedures.
cosmo Oliver Bembom Supervised detection of conserved motifs in DNA sequences
cosmoGUI Oliver Bembom GUI for constructing constraint sets used by the cosmo package
ctc Antoine Lucas Cluster and Tree Conversion.
daMA Jobst Landgrebe Efficient design and analysis of factorial two-colour microarray data
DEDS Yuanyuan Xiao Differential Expression via Distance Summary for Microarray Data
DFP Rodrigo Alvarez-Glez Gene Selection
diffGeneAnalysis Choudary Jagarlamudi Performs differential gene expression Analysis
domainsignatures Florian Hahne Geneset enrichment based on InterPro domain signatures
dualKS Eric J. Kort Dual KS Discriminant Analysis and Classification
edd Vince Carey expression density diagnostics
edgeR Mark Robinson Empirical analysis of digital gene expression data in R
exonmap Crispin Miller High level analysis of Affymetrix exon array data
factDesign Denise Scholtens Factorial designed microarray experiment analysis
fdrame Effi Kenigsberg FDR adjustments of Microarray Experiments (FDR-AME)
flowClust Raphael Gottardo Clustering for Flow Cytometry
gaga David Rossell GaGa hierarchical model for microarray data analysis
genefilter Biocore Team c/o BioC user list genefilter: methods for filtering genes from microarray experiments
GeneMeta Biocore Team c/o BioC user list MetaAnalysis for High Throughput Experiments
geneRecommender Greg Hather A gene recommender algorithm to identify genes coexpressed with a query set of genes
GeneSelector Martin Slawski GeneSelector
GGBase Vince Carey infrastructure for genetics of gene expression (c) 2008 VJ Carey
GGtools Vince Carey software and data for genetical genomics (c) 2006 VJ Carey
GlobalAncova R. Meister Calculates a global test for differential gene expression between groups
globaltest Jelle Goeman Testing Association of Groups of Genes with a Clinical Variable
GOstats Robert Gentleman Tools for manipulating GO and microarrays.
gpls Biocore Team c/o BioC user list Classification using generalized partial least squares
GraphAT Thomas LaFramboise Graph Theoretic Association Tests
GSEABase Biocore Team c/o BioC user list Gene set enrichment data structures and methods
GSEAlm Assaf Oron Linear Model Toolset for Gene Set Enrichment Analysis
HEM HyungJun Cho Heterogeneous error model for identification of differentially expressed genes under multiple conditions
hopach Katherine S. Pollard Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
Icens Biocore Team c/o BioC user list NPMLE for Censored and Truncated Data
impute Balasubramanian Narasimhan impute: Imputation for microarray data
iterativeBMA Ka Yee Yeung The Iterative Bayesian Model Averaging (BMA) algorithm
iterativeBMAsurv Ka Yee Yeung The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis
lapmix Yann Ruffieux Laplace Mixture Model in Microarray Experiments
LBE Cyril Dalmasso Estimation of the false discovery rate.
limma Gordon Smyth Linear Models for Microarray Data
limmaGUI Keith Satterley GUI for limma package
LMGene John Tillinghast LMGene Software for Date Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
logicFS Holger Schwender Identification of SNP Interactions
LPE Nitin Jain Methods for analyzing microarray data using Local Pooled Error (LPE) method
LPEadj Carl Murie A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.
maanova Hyuna Yang Tools for analyzing Micro Array experiments
made4 Aedin Culhane Multivariate analysis of microarray data using ADE4
maigesPack Gustavo H. Esteves Functions to handle cDNA microarray data, including several methods of data analysis
MantelCorr Brian Steinmeyer Compute Mantel Cluster Correlations
maSigPro Ana Conesa Significant Gene Expression Profile Differeneces in Time Course Microarray Data
MeasurementError.cor Beiying Ding Measurement Error model estimate for correlation coefficient
metaArray Hyungwon Choi Integration of Microarray Data for Meta-analysis
Mfuzz Matthias Futschik Soft clustering of time series gene expression data
microRNA Robert Gentleman Data and functions for dealing with microRNAs
MiPP Sukwoo Kim Misclassification Penalized Posterior Classification
miRNApath James M. Ward miRNApath: Pathway Enrichment for miRNA Expression Data
MLInterfaces V. Carey Uniform interfaces to R machine learning procedures for data in Bioconductor containers
multtest Katherine S. Pollard Resampling-based multiple hypothesis testing
nem Florian Markowetz Nested Effects Models to reconstruct phenotypic hierarchies
occugene Oliver Will Functions for Multinomial Occupancy Distribution
OCplus Alexander Ploner Operating characteristics plus sample size and local fdr for microarray experiments
oneChannelGUI Raffaele A Calogero This package extends the capabilities of affylmGUI graphical interface. Affymetrix 3' IVT, gene an exon arrays are actually implemented togheter with Illumina, GEO matrix series files and tab delimited files.
OrderedList Claudio Lottaz Similarities of Ordered Gene Lists
OutlierD Sukwoo Kim Outlier detection using quantile regression on the M-A scatterplots of high-throughput data
pamr Rob Tibshirani Pam: prediction analysis for microarrays
parody VJ Carey Parametric And Resistant Outlier DYtection
pcaMethods Wolfram Stacklies A collection of PCA methods.
pdmclass James W. MacDonald Classification of Microarray Samples using Penalized Discriminant Methods
plw Magnus Astrand Probe level Locally moderated Weighted t-tests.
puma Richard Pearson Propagating Uncertainty in Microarray Analysis
qvalue John D. Storey Q-value estimation for false discovery rate control
rbsurv Sooheang Eo Robust likelihood-based survival modeling with microarray data
rflowcyt N. LeMeur Statistical tools and data structures for analytic flow cytometry
rHVDM Martino Barenco Hidden Variable Dynamic Modeling
RNAither Nora Rieber Statistical analysis of high-throughput RNAi screens
ROC Vince Carey utilities for ROC, with uarray focus
Rtreemix Jasmina Bogojeska Rtreemix: Mutagenetic trees mixture models.
SAGx Per Broberg, Statistical Analysis of the GeneChip
seqLogo Oliver Bembom Sequence logos for DNA sequence alignments
sigPathway Weil Lai Pathway Analysis
SIM Maarten van Iterson Integrated Analysis of gene expression and copynumber data
simpleaffy Crispin Miller Very simple high level analysis of Affymetrix data
sizepower Weiliang Qiu Sample Size and Power Calculation in Micorarray Studies
SLqPCR Matthias Kohl Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH
sscore Richard Kennedy S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
ssize Gregory R. Warnes Estimate Microarray Sample Size
stam Claudio Lottaz Structured Analysis of Microarray Data
timecourse Yu Chuan Tai Statistical Analysis for Developmental Microarray Time Course Data
topGO Adrian Alexa topGO: Enrichment analysis for Gene Ontology
twilight Stefanie Scheid Estimation of local false discovery rate
VanillaICE Robert Scharpf Methods for fitting Hidden Markov Models to SNP chip data
vbmp Nicola Lama Variational Bayesian Multinomial Probit Regression
XDE Robert Scharpf XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression